# COexpression Tables ANalysis

## Documentation for package ‘COTAN’ version 2.8.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N O P R S T U V

## -- A --

addClusterization | Handling cells' _clusterization_ and related functions
addClusterization-method | Handling cells' _clusterization_ and related functions
addClusterizationCoex | Handling cells' _clusterization_ and related functions
addClusterizationCoex-method | Handling cells' _clusterization_ and related functions
addCondition | Handling cells' _conditions_ and related functions
addCondition-method | Handling cells' _conditions_ and related functions
addElementToMetaDataset | Handling _meta-data_ in 'COTAN' objects
addElementToMetaDataset-method | Handling _meta-data_ in 'COTAN' objects
AdvancedGDIUniformityCheck-class | Definition of the *Transcript Uniformity Checker* classes
asClusterization | _Clusters_ utilities
automaticCOTANObjectCreation | 'COTAN' shortcuts

## -- B --

BaseUniformityCheck-class | Definition of the *Transcript Uniformity Checker* classes

## -- C --

calcDist | Numeric Utilities
calculateCoex | Calculating the COEX matrix for genes and cells
calculateCoex-method | Calculating the COEX matrix for genes and cells
calculateG | Calculating the COEX matrix for genes and cells
calculateGDI | Calculations of genes statistics
calculateGDIGivenCorr | Calculations of genes statistics
calculateGDIGivenS | Calculations of genes statistics
calculateGenesCE | Calculations of genes statistics
calculateLikelihoodOfObserved | Calculating the COEX matrix for genes and cells
calculateMu | Calculating the COEX matrix for genes and cells
calculatePartialCoex | Calculating the COEX matrix for genes and cells
calculatePDI | Calculations of genes statistics
calculatePValue | Calculations of genes statistics
calculateS | Calculating the COEX matrix for genes and cells
calculateThresholdShiftToUniformity | Definition of the *Transcript Uniformity Checker* classes
calculateThresholdShiftToUniformity-method | Definition of the *Transcript Uniformity Checker* classes
CalculatingCOEX | Calculating the COEX matrix for genes and cells
canUseTorch | Handling Multi-Core and GPU environments
cellsHeatmapPlot | Heatmap Plots
cellSizePlot | Raw data cleaning
cellsUMAPPlot | Handling cells' _clusterization_ and related functions
cellsUniformClustering | Uniform Clusters
checkClusterUniformity | Uniform Clusters
checkersToDF | Definition of the *Transcript Uniformity Checker* classes
checkObjIsUniform | Definition of the *Transcript Uniformity Checker* classes
checkObjIsUniform-method | Definition of the *Transcript Uniformity Checker* classes
clean | Raw data cleaning
clean-method | Raw data cleaning
cleanPlots | Raw data cleaning
clusterGeneContingencyTables | Handling cells' _clusterization_ and related functions
clustersDeltaExpression | Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions
ClustersList | _Clusters_ utilities
clustersMarkersHeatmapPlot | Handling cells' _clusterization_ and related functions
clustersSummaryData | Handling cells' _clusterization_ and related functions
clustersSummaryPlot | Handling cells' _clusterization_ and related functions
clustersTreePlot | Handling cells' _clusterization_ and related functions
conditionsFromNames | Handle names and factors' levels
contingencyTables | Calculating the COEX matrix for genes and cells
Conversions | Data class conversions
convertFromSingleCellExperiment | Data class conversions
convertToSingleCellExperiment | Data class conversions
COTAN | 'COTAN' shortcuts
COTAN-class | Definition of the 'COTAN' class
COTAN_coerce_to_scCOTAN | Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions
COTAN_Legacy | Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions
COTAN_ObjectCreation | 'COTAN' shortcuts

## -- D --

Datasets | Data-sets
datasetTags | Handling _meta-data_ in 'COTAN' objects
DEAOnClusters | Handling cells' _clusterization_ and related functions
dfToCheckers | Definition of the *Transcript Uniformity Checker* classes
dispersionBisection | Numeric Utilities
distancesBetweenClusters | Handling cells' _clusterization_ and related functions
dropCellsCoex | Calculating the COEX matrix for genes and cells
dropCellsCoex-method | Calculating the COEX matrix for genes and cells
dropClusterization | Handling cells' _clusterization_ and related functions
dropClusterization-method | Handling cells' _clusterization_ and related functions
dropCondition | Handling cells' _conditions_ and related functions
dropCondition-method | Handling cells' _conditions_ and related functions
dropGenesCells | Raw data cleaning
dropGenesCells-method | Raw data cleaning
dropGenesCoex | Calculating the COEX matrix for genes and cells
dropGenesCoex-method | Calculating the COEX matrix for genes and cells

## -- E --

ECDPlot | Raw data cleaning
ERCCraw | Data-sets
establishGenesClusters | Calculations of genes statistics
estimateDispersionBisection | Estimation of the 'COTAN' model's parameters
estimateDispersionBisection-method | Estimation of the 'COTAN' model's parameters
estimateDispersionNuBisection | Estimation of the 'COTAN' model's parameters
estimateDispersionNuBisection-method | Estimation of the 'COTAN' model's parameters
estimateDispersionNuNlminb | Estimation of the 'COTAN' model's parameters
estimateDispersionNuNlminb-method | Estimation of the 'COTAN' model's parameters
estimateLambdaLinear | Estimation of the 'COTAN' model's parameters
estimateLambdaLinear-method | Estimation of the 'COTAN' model's parameters
estimateNuBisection | Estimation of the 'COTAN' model's parameters
estimateNuBisection-method | Estimation of the 'COTAN' model's parameters
estimateNuLinear | Estimation of the 'COTAN' model's parameters
estimateNuLinear-method | Estimation of the 'COTAN' model's parameters
estimateNuLinearByCluster | Handling cells' _clusterization_ and related functions
estimateNuLinearByCluster-method | Handling cells' _clusterization_ and related functions
estimatorsAreReady | Estimation of the 'COTAN' model's parameters
expectedContingencyTables | Calculating the COEX matrix for genes and cells
expectedContingencyTablesNN | Calculating the COEX matrix for genes and cells
expectedPartialContingencyTables | Calculating the COEX matrix for genes and cells
expectedPartialContingencyTablesNN | Calculating the COEX matrix for genes and cells

## -- F --

factorToVector | Handle names and factors' levels
findClustersMarkers | Handling cells' _clusterization_ and related functions
findFullyExpressedGenes | Raw data cleaning
findFullyExpressedGenes-method | Raw data cleaning
findFullyExpressingCells | Raw data cleaning
findFullyExpressingCells-method | Raw data cleaning
flagNotFullyExpressedGenes | Raw data cleaning
flagNotFullyExpressedGenes-method | Raw data cleaning
flagNotFullyExpressingCells | Raw data cleaning
flagNotFullyExpressingCells-method | Raw data cleaning
fromClustersList | _Clusters_ utilities
funProbZero | Numeric Utilities

## -- G --

GDICheck-class | Definition of the *Transcript Uniformity Checker* classes
GDIPlot | Uniform Clusters
genesCoexSpace | Calculations of genes statistics
geneSetEnrichment | Handling cells' _clusterization_ and related functions
genesHeatmapPlot | Heatmap Plots
genesSizePlot | Raw data cleaning
GenesStatistics | Calculations of genes statistics
getAllConditions | Handling cells' _conditions_ and related functions
getAllConditions-method | Handling cells' _conditions_ and related functions
getCells | Raw data 'COTAN' accessors
getCells-method | Raw data 'COTAN' accessors
getCellsCoex | Calculating the COEX matrix for genes and cells
getCellsCoex-method | Calculating the COEX matrix for genes and cells
getCellsSize | Raw data 'COTAN' accessors
getCellsSize-method | Raw data 'COTAN' accessors
getCheckerThreshold | Definition of the *Transcript Uniformity Checker* classes
getCheckerThreshold-method | Definition of the *Transcript Uniformity Checker* classes
getClusterizationData | Handling cells' _clusterization_ and related functions
getClusterizationData-method | Handling cells' _clusterization_ and related functions
getClusterizationName | Handling cells' _clusterization_ and related functions
getClusterizationName-method | Handling cells' _clusterization_ and related functions
getClusterizations | Handling cells' _clusterization_ and related functions
getClusterizations-method | Handling cells' _clusterization_ and related functions
getClusters | Handling cells' _clusterization_ and related functions
getClustersCoex | Handling cells' _clusterization_ and related functions
getClustersCoex-method | Handling cells' _clusterization_ and related functions
getColorsVector | getColorsVector
getColumnFromDF | Handling _meta-data_ in 'COTAN' objects
getCondition | Handling cells' _conditions_ and related functions
getCondition-method | Handling cells' _conditions_ and related functions
getConditionName | Handling cells' _conditions_ and related functions
getConditionName-method | Handling cells' _conditions_ and related functions
getDataMatrix | Calculating the COEX matrix for genes and cells
getDims | Handling _meta-data_ in 'COTAN' objects
getDims-method | Handling _meta-data_ in 'COTAN' objects
getDispersion | Estimation of the 'COTAN' model's parameters
getDispersion-method | Estimation of the 'COTAN' model's parameters
getFullyExpressedGenes | Raw data cleaning
getFullyExpressedGenes-method | Raw data cleaning
getFullyExpressingCells | Raw data cleaning
getFullyExpressingCells-method | Raw data cleaning
getGDI | Calculations of genes statistics
getGDI-method | Calculations of genes statistics
getGenes | Raw data 'COTAN' accessors
getGenes-method | Raw data 'COTAN' accessors
getGenesCoex | Calculating the COEX matrix for genes and cells
getGenesCoex-method | Calculating the COEX matrix for genes and cells
getGenesSize | Raw data 'COTAN' accessors
getGenesSize-method | Raw data 'COTAN' accessors
getLambda | Estimation of the 'COTAN' model's parameters
getLambda-method | Estimation of the 'COTAN' model's parameters
getLogNormData | Estimation of the 'COTAN' model's parameters
getMetadataCells | Handling _meta-data_ in 'COTAN' objects
getMetadataCells-method | Handling _meta-data_ in 'COTAN' objects
getMetadataDataset | Handling _meta-data_ in 'COTAN' objects
getMetadataDataset-method | Handling _meta-data_ in 'COTAN' objects
getMetadataElement | Handling _meta-data_ in 'COTAN' objects
getMetadataElement-method | Handling _meta-data_ in 'COTAN' objects
getMetadataGenes | Handling _meta-data_ in 'COTAN' objects
getMetadataGenes-method | Handling _meta-data_ in 'COTAN' objects
getMetaInfoRow | Handling _meta-data_ in 'COTAN' objects
getMu | Calculating the COEX matrix for genes and cells
getNormalizedData | Estimation of the 'COTAN' model's parameters
getNu | Estimation of the 'COTAN' model's parameters
getNu-method | Estimation of the 'COTAN' model's parameters
getNumCells | Raw data 'COTAN' accessors
getNumCells-method | Raw data 'COTAN' accessors
getNumExpressedGenes | Raw data 'COTAN' accessors
getNumExpressedGenes-method | Raw data 'COTAN' accessors
getNumGenes | Raw data 'COTAN' accessors
getNumGenes-method | Raw data 'COTAN' accessors
getNumOfExpressingCells | Raw data 'COTAN' accessors
getNumOfExpressingCells-method | Raw data 'COTAN' accessors
getNuNormData | Estimation of the 'COTAN' model's parameters
getProbabilityOfZero | Estimation of the 'COTAN' model's parameters
getRawData | Raw data 'COTAN' accessors
getRawData-method | Raw data 'COTAN' accessors
getSelectedGenes | Calculating the COEX matrix for genes and cells
getZeroOneProj | Raw data 'COTAN' accessors
getZeroOneProj-method | Raw data 'COTAN' accessors
groupByClusters | _Clusters_ utilities
groupByClustersList | _Clusters_ utilities

## -- H --

HandleMetaData | Handling _meta-data_ in 'COTAN' objects
handleMultiCore | Handling Multi-Core and GPU environments
handleNamesSubsets | Handle names and factors' levels
HandleStrings | Handle names and factors' levels
HandlingClusterizations | Handling cells' _clusterization_ and related functions
HandlingConditions | Handling cells' _conditions_ and related functions
heatmapPlot | Heatmap Plots
HeatmapPlots | Heatmap Plots

## -- I --

initializeMetaDataset | Handling _meta-data_ in 'COTAN' objects
initializeMetaDataset-method | Handling _meta-data_ in 'COTAN' objects
Installing_torch | Installing torch R library (on Linux)
isCoexAvailable | Calculating the COEX matrix for genes and cells
isCoexAvailable-method | Calculating the COEX matrix for genes and cells
isEmptyName | Handle names and factors' levels

## -- L --

logFoldChangeOnClusters | Handling cells' _clusterization_ and related functions
LoggingFunctions | Logging in the 'COTAN' package
logThis | Logging in the 'COTAN' package

## -- M --

mat2vec_rfast | Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions
mergeClusters | _Clusters_ utilities
mergeUniformCellsClusters | Uniform Clusters
mitochondrialPercentagePlot | Raw data cleaning
multiMergeClusters | _Clusters_ utilities
MultiThreading | Handling Multi-Core and GPU environments

## -- N --

niceFactorLevels | Handle names and factors' levels
normalizeNameAndLabels | Handling cells' _conditions_ and related functions
nuBisection | Numeric Utilities
NumericUtilities | Numeric Utilities

## -- O --

observedContingencyTables | Calculating the COEX matrix for genes and cells
observedContingencyTablesYY | Calculating the COEX matrix for genes and cells
observedPartialContingencyTables | Calculating the COEX matrix for genes and cells
observedPartialContingencyTablesYY | Calculating the COEX matrix for genes and cells

## -- P --

parallelDispersionBisection | Numeric Utilities
parallelNuBisection | Numeric Utilities
ParametersEstimations | Estimation of the 'COTAN' model's parameters
plotTheme | Heatmap Plots
proceedToCoex | 'COTAN' shortcuts
proceedToCoex-method | 'COTAN' shortcuts
pValueFromDEA | Handling cells' _clusterization_ and related functions

## -- R --

raw.dataset | Data-sets
RawDataCleaning | Raw data cleaning
RawDataGetters | Raw data 'COTAN' accessors
reorderClusterization | Handling cells' _clusterization_ and related functions

## -- S --

scatterPlot | Raw data cleaning
scCOTAN-class | Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions
scCotan_coerce_to_COTAN | Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions
screePlot | Raw data cleaning
setColumnInDF | Handling _meta-data_ in 'COTAN' objects
setLoggingFile | Logging in the 'COTAN' package
setLoggingLevel | Logging in the 'COTAN' package
shiftCheckerThresholds | Definition of the *Transcript Uniformity Checker* classes
shiftCheckerThresholds-method | Definition of the *Transcript Uniformity Checker* classes
SimpleGDIUniformityCheck-class | Definition of the *Transcript Uniformity Checker* classes
singleHeatmapDF | Heatmap Plots
storeGDI | Calculations of genes statistics
storeGDI-method | Calculations of genes statistics

## -- T --

test.dataset | Data-sets
test.dataset.clusters1 | Data-sets
test.dataset.clusters2 | Data-sets
toClustersList | _Clusters_ utilities

## -- U --

UMAPPlot | Handling cells' _clusterization_ and related functions
UniformClusters | Uniform Clusters
UniformTranscriptCheckers | Definition of the *Transcript Uniformity Checker* classes
updateMetaInfo | Handling _meta-data_ in 'COTAN' objects

## -- V --

vec2mat_rfast | Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions
vignette.merge.clusters | Data-sets
vignette.merge2.clusters | Data-sets
vignette.split.clusters | Data-sets